Sign in

Bede Constantinides

@bede.im
1K followers 1.6K following 213 posts

Research fellow at the University of Birmingham interested in infectious disease informatics. Also cycling, photography, active travel. bede.im

PostsRepliesMedia
Bede Constantinides @bede.im · 29/09/2026
"An estimated 2.3 million new cancer cases were attributable to infections globally in 2024… Equivalent to 12% of all cancer cases" www.thelancet.com/journals/lan...
thelancet.com
Global burden of cancer attributable to infections in 2024: a worldwide incidence analysis
Our findings highlight the importance of infection control to achieve cancer prevention. Scientifically proven, but often underused, approaches include HPV and HBV vaccination; testing and treatment o...
031
Bede Constantinides @bede.im · 27/09/2026
Celebrated road cycling world champs with a mates race of ~20 riders in a double breakaway scenario. Podium secured for team Norway inc @nickdsandy.bsky.social 🇳🇴
152
Bede Constantinides @bede.im · 24/09/2026
Josh (@scalene.bsky.social) and I asked the best open-weight models a tricky molecular biology research question that Opus 5.5 refuses. Josh graded each answer, and DeepSeek V4 Pro and Kimi K3 both beat Opus 5, taking less time and costing less. Blogged: bede.im/2026/09/24/o...
bede.im
Asking open models about molecular biology
293
Reposted by Bede Constantinides
Conor (Conchúr) Meehan @conmeehan.bsky.social · 23/09/2026
We are looking for someone with a strong background in metagenomics and epidemiology to join our team for ~2 years at UKHSA to work on the mSCAPE programme. Please see (and share) the link below and feel free to message me with any enquiries. www.healthjobsuk.com/job/Canary_W...
healthjobsuk.com
Job vacancy: Senior Scientist (Epidemiology), UK Health Security Agency, Canary Wharf, London | trac.jobs
0510
Bede Constantinides @bede.im · 23/09/2026
This is a big deal for virus data sharing. Submitters can now upload raw reads, immediately share them with collaborators, and let Pathoplexus take care of the INSDC submission process on their behalf…
1101
Reposted by Bede Constantinides
Pathoplexus @pathoplexus.org · 22/09/2026
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences! Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses. 📰 Read more: pathoplexus.org/news/2026-09...
AI-generated image showing raw reads (short reads) lining up above a consensus sequence, with both the raw reads and consensus sequence labelled. Vague images below show a virus, coverage, and DNA.
32610
Reposted by Bede Constantinides
Nick Loman @pathogenomenick.bsky.social · 22/09/2026
Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...
climb.ac.uk
Call for Applications: GPU-Accelerated Computing for Microbiome and Metagenomic Research · CLIMB
CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...
31920
Reposted by Bede Constantinides
Richard Sever @richardsever.bsky.social · 20/09/2026
"All corners of academia will soon be flooded with AI-generated research....Maths and CS go first because their entire output is symbol manipulation...Biology comes later not because biologists are cleverer but because the rate-limiting step is physical" giorgio.gilest.ro/the-weimar-o...
giorgio.gilest.ro
The Weimar of knowledge – la bottega
56640
Reposted by Bede Constantinides
Will Matlock @wtmatlock.bsky.social · 09/09/2026
Does an AMR gene on a plasmid diversify differently to an AMR gene on a chromosome? We are looking for a PhD student to work on this question in Bath!
gw4biomed.ac.uk
Turning up the volume: plasmid copy number and gene duplications as drivers of antimicrobial resistance evolution - GW4 BioMed MRC DTP
Project Code IIAR27Ba Matlock Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Plasmids are important drivers of antimicrobial res...
12627
Reposted by Bede Constantinides
Zamin Iqbal @zaminiqbal.bsky.social · 09/09/2026
More than a decade since Mykrobe first came out - v happy @martibartfast.bsky.social has developed a Go version, which means we could revive the old app, which always made it much more accessible. Same results as Mykrobe but faster.
0123
Reposted by Bede Constantinides
Stefan Neumann @neumannstefan.com · 08/09/2026
I wanted to submit a grant proposal this week and ended up not doing it precisely because of this. I have no idea how in a project that, say, lasts from 2027 to 2032, I can promise results that cannot be achieved by an LLM in 2031 with one person prompting.
1103
Reposted by Bede Constantinides
Ethan Mollick @emollick.bsky.social · 08/09/2026
This is a VERY big one. (And yes, the fights over academic credit and what happened in the race for the proof needs to be resolved, but it is still appears that this is a big one, if true.) openai.com/index/navier...
openai.com
On the Navier–Stokes Millennium Prize Problem
We’re sharing an AI-generated solution to the Navier–Stokes Millennium Prize Problem, including a writeup and a formal proof in Lean.
619731
Bede Constantinides @bede.im · 01/09/2026
Reason #617 cyclists don't use cycle lanes
110
Reposted by Bede Constantinides
Richard Sever @richardsever.bsky.social · 27/08/2026
$3.7 billion spent on APCs in 2025. That's ~1000X more than it costs to run bioRxiv/medRxiv. Worth thinking about as we consider how to fund infrastructure... arxiv.org/pdf/2608.16322
arxiv.org
813378
Reposted by Bede Constantinides
Pathoplexus @pathoplexus.org · 26/08/2026
1/ 🦟 New on @Pathoplexus: Zika virus (ZIKV) is now supported! Share your ZIKV sequences as Open or Restricted-Use, just like our other pathogens. Read more: pathoplexus.org/news/2026-08... 📰
Screenshot of the Pathoplexus website homepage, where the new Zika virus button is circled in red
2167
Bede Constantinides @bede.im · 26/08/2026
"Load-bearing"
110
Reposted by Bede Constantinides
Philipp Markolin @philippmarkolin.eurosky.social · 18/08/2026
In 2026, there is no longer any lab leak hypothesis you can state consistently with the available evidence. Despite this, it has been the dominant media narrative for six years. Read my new data-driven investigation: www.protagonist-science.com/p/biased-med...
protagonist-science.com
Biased media coverage and the lab leak theory
Gain-of-function fearmongering and blame gets the glitzy NYT visual treatment as Republicans weaponize the lab leak theory again in attacks on Dr. Anthony Fauci
12342142
Bede Constantinides @bede.im · 20/08/2026
"Smoke test"
030
Reposted by Bede Constantinides
Neil Miles @neilsmiles.com · 17/08/2026
29th August 1985 - An excited Michael Fish gets to deploy the rarely seen red number as the temperature gets up to an incredible 26 degrees in London!
521655713
Bede Constantinides @bede.im · 18/08/2026
As requested, Deacon 0.17.0 adds BINSEQ CBQ support. CBQ is a binary sequence format by @noamteyssier.bsky.social that’s tiny on disk, fast to decode, and supports Ns. With CBQ, Deacon can filter sequences at >5 Gbp/s on a laptop (faster than uncompressed FASTA) github.com/bede/deacon/...
Comparison of Deacon host depletion throughput for cbq, cba, fasta, fastq and fastq.gz for simulated viral reads, with varying thread counts.
193
Bede Constantinides @bede.im · 15/08/2026
Awful news: "Tarling was hit by ​a non-race car driving in the opposite ​direction."
000
Reposted by Bede Constantinides
TCTMD @tctmd.bsky.social · 12/08/2026
David Taggart, Cardiovascular Surgeon and ‘Staunch Truthteller,’ Dies at 69
tctmd.com
David Taggart, Cardiovascular Surgeon and ‘Staunch Truthteller,’ Dies at 69
David Taggart, Cardiovascular Surgeon and ‘Staunch Truthteller,’ Dies at 69 mosbey@crf.org Wed, 08/12/2026 - 16:02 Yael L. Maxwell Known for his honesty and for igniting controversy, Taggart will be remembered for always putting patient interests first.
001
Bede Constantinides @bede.im · 08/08/2026
I get that airlines oversell flights, but should it not be illegal to pretend that check-in failed due to "technical issues" rather than running out of seats due to overselling? And then to advise checking in at airport when there's negligible chance of flying. Easyjet.
030
Reposted by Bede Constantinides
Kelly Sovacool @kelly.sova.cool · 06/08/2026
hot take: it is better not to have an image/graphic at all for your blog/talk/flyer/poster than to make one with genAI
0115
Reposted by Bede Constantinides
Aris Katzourakis @ariskatzourakis.bsky.social · 06/08/2026
HIV's hidden history: New study reveals much deeper roots stretching back millions of years sciencex.com/news/2026-07...
sciencex.com
HIV's hidden history: New study reveals much deeper roots stretching back millions of years
Researchers used to think that HIV and its relatives were pretty recent things, maybe only a few hundred years old. But a growing body of evidence now suggests their history is far more ancient, with ...
22112
Bede Constantinides @bede.im · 31/07/2026
This will make indexing k-mers in e.g. HPRC (human) and GTDB (bacteria) a breeze
030
Reposted by Bede Constantinides
Ragnar {Groot Koerkamp} @curiouscoding.nl · 31/07/2026
I've been working on Pandedup the past weeks: a tool to quickly dedup the k-mer content of a pangenome (read: HPRCv2). Just uploaded a k=64 SPSS (k-mer spectrum preserving string set) as well: zenodo.org/records/2172... This reduces the ~1.5Tbp input to just 10.6Gbp. github.com/RagnarGrootK...
github.com
GitHub - RagnarGrootKoerkamp/pandedup: Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome.
Pandedup uses minimizers to build a quick & dirty k-mer spectrum (SPSS) from a .AGC pangenome. - RagnarGrootKoerkamp/pandedup
1104
Reposted by Bede Constantinides
bioRxiv Genomics @biorxiv-genomic.bsky.social · 22/07/2026
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation www.biorxiv.org/content/10.64898/20…
04024
Reposted by Bede Constantinides
Random Tiling Bot @randomtiling.bsky.social · 19/07/2026
This image shows a random tiling of a square created by the Random Tiling Bot
021
Reposted by Bede Constantinides
Ragnar {Groot Koerkamp} @curiouscoding.nl · 13/07/2026
Also, Deacon was the motivation for engineering the k-PHF Hash Set! bsky.app/profile/curi...
021
Reposted by Bede Constantinides
Ragnar {Groot Koerkamp} @curiouscoding.nl · 09/07/2026
My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders
2168
Reposted by Bede Constantinides
Antoine Limasset @npmalfoy.bsky.social · 04/02/2026
Preprint alert! arxiv.org/abs/2602.03525 TLDR: ZOR filters are STATIC filters with false positives. -Almost memory optimal: <1% overhead over the theoretical lower bound (!!!) -Fast queries: ~100 ns -Construction cannot fail A thread:
arxiv.org
ZOR filters: fast and smaller than fuse filters
Probabilistic membership filters support fast approximate membership queries with a controlled false-positive probability $\varepsilon$ and are widely used across storage, analytics, networking, and b...
13413
Bede Constantinides @bede.im · 13/07/2026
Ever wanted to quickly check host content of DNA sequences? bede.im/sapiometer
12010
Reposted by Bede Constantinides
ARTIC network @artic.network · 09/07/2026
139 genomes now sequenced from the ongoing 2026 Bundibugyo virus disease outbreak in DRC, spanning 16 Health Zones. Led by INRB with support from the ARTIC network (Wellcome Trust and Gates Foundation). Full analysis: virological.org/t/genomic-ep...
virological.org
Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo
Genomic epidemiology of the ongoing 2026 Bundibugyo Virus Disease outbreak in the Democratic Republic of the Congo Institut National de Recherche Biomédicale (INRB), Kinshasa – DRC and partners Conte...
1189
Bede Constantinides @bede.im · 04/07/2026
"You gather your most expensive people into a room to make your most important decisions. Then, somewhere in the second hour, the room quietly gets worse at making them. Not the people. The room."
blog.mikebowler.ca
The bottleneck might be the air in the room
You gather your most expensive people into a room to make your most important decisions. Then, somewhere in the second hour, the room quietly gets worse at making them. Not the people. The room.
141
Reposted by Bede Constantinides
ARTIC network @artic.network · 01/07/2026
Important read from ARTIC PI Placide Mbala (INRB) and @krutikakuppalli.bsky.social in @statnews.com, on what the Bundibugyo Ebola outbreak reveals about the limits of pathogen-specific diagnostics, and why we need pathogen-agnostic systems for the next emergency www.statnews.com/2026/07/01/e...
statnews.com
What Ebola and Marburg are teaching us about the next pandemic
“What is urgently needed is a shift from pathogen-specific diagnostics toward pathogen-agnostic diagnostic systems,” write Krutika Kuppalli and Placide Mbala.
01510
Reposted by Bede Constantinides
ARTIC network @artic.network · 30/06/2026
Excellent update from @pathoplexus.org this month. Pathoplexus has been central to data sharing during the ongoing Bundibugyo ebolavirus outbreak response, with ARTIC contributing developer time to Loculus, the platform behind it.
073
Bede Constantinides @bede.im · 25/06/2026
Air conditioning is not ventilation. Crisp and dry conditioned air feels fresh but often isn't. Beware of this sensory trickery.
050
Reposted by Bede Constantinides
James Hay @jameshay.bsky.social · 22/06/2026
Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
0515
Reposted by Bede Constantinides
Johanna von Wachsmann @johannavw.bsky.social · 16/06/2026
🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...
06124
Reposted by Bede Constantinides
The Guardian @theguardian.com · 12/06/2026
Emergency hospital admissions fell after introduction of London’s T-charge and Ulez, study suggests
theguardian.com
Emergency hospital admissions fell after introduction of London’s T-charge and Ulez, study suggests
Imperial College scientists analysed health records before and after introduction of air pollution reduction zones Low emission and clean air zones attract controversy whenever they are proposed, but there is growing evidence that they work in improving air quality. The Bradford zone was followed by a reduction of about 25% in GP visits for heart and breathing problems and survey data shows that the central London zone was followed by a reduction in the likelihood of a person taking sick leave. Now analysis of health records has found emergency admissions to hospital reduced after the introduction of the T-charge and ultra-low emissions zone (Ulez) in central London. Continue reading...
12413194
Bede Constantinides @bede.im · 11/06/2026
Never have I seen the car/road metaphor pushed this hard
anthropic.com
Paving the way for agents in biology
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
010
Reposted by Bede Constantinides
Ryan Wick @rrwick.bsky.social · 11/06/2026
New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...
rrwick.github.io
Dorado v2.0.0: no more sup?
a blog for miscellaneous bioinformatics stuff
15526
Bede Constantinides @bede.im · 07/06/2026
"On-board Wi-Fi was also tested by Ofcom and it performed well just one percent of the time."
030
Bede Constantinides @bede.im · 05/06/2026
#r4today @drtedros.who.int: "While investing in defence… Please don't forget the common enemy that we have: a virus that doesn't care about our borders, our politics, or about whatever excuses we have. We have to be also prepared for that." www.bbc.co.uk/sounds/play/...
bbc.co.uk
Today - 05/06/2026 - BBC Sounds
News and current affairs, including Sports Desk, Weather and Thought for the Day.
061
Reposted by Bede Constantinides
Ragnar {Groot Koerkamp} @curiouscoding.nl · 04/06/2026
Now that Sassy had been published and presented, it's time for it to break out of my bubble :) curiouscoding.nl/posts/sassy/ www.reddit.com/r/rust/comme...
197
Reposted by Bede Constantinides
ARTIC network @artic.network · 01/06/2026
The ARTIC Primer Foundry is now live and will soon begin shipping BDBV primers on request primalscheme.com/orders
primalscheme.com
PrimalScheme: primer panels for multiplex PCR
PrimalScheme is a tool for designing primer panels for multiplex PCR. It uses a greedy algorithm to find primers for tiling amplicon generation for multiple reference genomes.
088
Reposted by Bede Constantinides
ARTIC network @artic.network · 01/06/2026
ARTIC network has published Bundibugyo (BDBV) sequencing resources as the 2026 outbreak continues in DRC & Uganda. We have compiled guidance for labs wishing to sequence, assemble and analyse BDBV genomes: artic.network/viruses/bdbv/bdbv-sequencing-guide.html
artic.network
Bundibugyo virus genomic sequencing resources | ARTIC network - pathogen genomics from sample to response
12613
Reposted by Bede Constantinides
Chris Newfield @cnewf.bsky.social · 25/05/2026
the FT has two pieces on the slow-motion collapse of UK higher ed. 4/5ths of unis are doing voluntary layoffs; 38% are doing compulsory. Meanwhile Britain and its flatlined productivity growth sleepwalks through its unprecedented loss of advanced capabilities www.ft.com/content/8097...
8228137
Reposted by Bede Constantinides
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 30/05/2026
Memory-safe high-performance sequence mapping with rammap www.biorxiv.org/content/10.64898/20…
12613